FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: 2G4GR
Calculation Name: 7S1K-h-Other547
Preferred Name:
Target Type:
Ligand Name: radezolid | n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 5'-o-(dihydroxyphosphanyl)-2,8-dimethyladenosine | 2n-methylguanosine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | (1s)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid
Ligand 3-letter code: RD8 | G7M | 1MG | 8AH | 2MG | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | H2U | OMC | OMU | 4D4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7S1K
Chain ID: h
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 58 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -306067.722389 |
|---|---|
| FMO2-HF: Nuclear repulsion | 283695.115623 |
| FMO2-HF: Total energy | -22372.606766 |
| FMO2-MP2: Total energy | -22437.91889 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)
Summations of interaction energy for
fragment #1(A:2:ALA)
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| -25.858 | -20.502 | 5.785 | -5.177 | -5.964 | -0.048 |
Interaction energy analysis for fragmet #1(A:2:ALA)
| frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | A | 4 | THR | 0 | 0.037 | 0.009 | 3.374 | -3.914 | -2.150 | 0.020 | -0.874 | -0.910 | -0.002 |
| 38 | A | 39 | GLU | -1 | -0.805 | -0.904 | 2.277 | -40.746 | -40.695 | 1.205 | -0.449 | -0.806 | 0.000 |
| 39 | A | 40 | ASP | -1 | -0.833 | -0.908 | 2.322 | -76.364 | -73.261 | 3.983 | -3.580 | -3.506 | -0.045 |
| 40 | A | 41 | THR | 0 | 0.025 | 0.007 | 2.474 | 3.241 | 3.679 | 0.578 | -0.259 | -0.757 | -0.001 |
| 41 | A | 42 | PRO | 0 | 0.060 | 0.010 | 4.629 | 4.674 | 4.674 | -0.001 | -0.015 | 0.015 | 0.000 |
| 4 | A | 5 | ILE | 0 | -0.033 | -0.002 | 6.013 | 0.674 | 0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | LYS | 1 | 0.886 | 0.942 | 7.846 | 22.460 | 22.460 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | ILE | 0 | 0.016 | 0.009 | 11.213 | 0.636 | 0.636 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | THR | 0 | 0.003 | -0.006 | 13.740 | 0.735 | 0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | GLN | 0 | -0.014 | 0.010 | 17.475 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | THR | 0 | 0.015 | -0.005 | 20.184 | 0.503 | 0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | ARG | 1 | 0.909 | 0.951 | 23.027 | 12.085 | 12.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | SER | 0 | 0.049 | 0.033 | 24.752 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | ALA | 0 | 0.074 | 0.013 | 24.746 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | ILE | 0 | 0.033 | 0.022 | 26.634 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | GLY | 0 | 0.046 | 0.027 | 30.377 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | ARG | 1 | 0.856 | 0.953 | 25.454 | 10.797 | 10.797 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | LEU | 0 | 0.097 | 0.051 | 26.287 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | PRO | 0 | 0.057 | 0.023 | 25.938 | -0.412 | -0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LYS | 1 | 1.009 | 1.001 | 21.977 | 12.159 | 12.159 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | HIS | 0 | 0.049 | 0.033 | 21.627 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | LYS | 1 | 0.857 | 0.918 | 21.342 | 9.994 | 9.994 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | ALA | 0 | 0.032 | 0.014 | 21.323 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | THR | 0 | -0.028 | -0.017 | 16.668 | -0.698 | -0.698 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | LEU | 0 | -0.016 | -0.014 | 16.777 | -0.815 | -0.815 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | LEU | 0 | -0.003 | 0.001 | 17.590 | -0.548 | -0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | GLY | 0 | 0.023 | 0.011 | 15.821 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | LEU | 0 | -0.010 | -0.002 | 11.939 | -1.290 | -1.290 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | GLY | 0 | 0.027 | 0.026 | 13.769 | -0.867 | -0.867 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | LEU | 0 | -0.062 | -0.025 | 15.966 | 0.540 | 0.540 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ARG | 1 | 0.945 | 0.960 | 18.322 | 14.251 | 14.251 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | ARG | 1 | 0.960 | 0.983 | 22.030 | 12.855 | 12.855 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ILE | 0 | 0.009 | -0.001 | 22.528 | -0.508 | -0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | GLY | 0 | 0.026 | 0.018 | 22.709 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | HIS | 0 | -0.067 | -0.023 | 18.359 | 0.237 | 0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | THR | 0 | 0.028 | -0.008 | 15.560 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | VAL | 0 | -0.086 | -0.041 | 12.799 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | GLU | -1 | -0.772 | -0.864 | 9.599 | -24.115 | -24.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | ARG | 1 | 0.809 | 0.891 | 7.608 | 23.926 | 23.926 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | ALA | 0 | 0.020 | 0.025 | 7.842 | 2.866 | 2.866 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | ILE | 0 | 0.017 | 0.018 | 6.522 | 3.135 | 3.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | ARG | 1 | 0.771 | 0.850 | 7.448 | 31.579 | 31.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | GLY | 0 | 0.028 | 0.012 | 10.141 | 2.066 | 2.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | MET | 0 | -0.040 | -0.021 | 11.589 | 2.028 | 2.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | ILE | 0 | 0.028 | 0.006 | 10.061 | 1.397 | 1.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | ASN | 0 | -0.004 | -0.002 | 13.806 | 1.650 | 1.650 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | ALA | 0 | -0.005 | 0.013 | 16.158 | 1.066 | 1.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | VAL | 0 | -0.022 | -0.030 | 17.174 | 1.040 | 1.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | SER | 0 | 0.022 | 0.018 | 17.567 | 0.507 | 0.507 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | PHE | 0 | 0.017 | 0.016 | 18.859 | 0.330 | 0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | MET | 0 | -0.121 | -0.062 | 21.216 | 0.847 | 0.847 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | VAL | 0 | 0.030 | 0.019 | 16.076 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | LYS | 1 | 0.818 | 0.903 | 17.161 | 16.962 | 16.962 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | VAL | 0 | 0.014 | -0.001 | 11.832 | -0.466 | -0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | GLU | -1 | -0.897 | -0.942 | 12.978 | -16.619 | -16.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | GLU | -2 | -1.665 | -1.789 | 9.620 | -53.154 | -53.154 | 0.000 | 0.000 | 0.000 | 0.000 |